Related papers: Autocatalytic systems and recombination: a reactio…
This work concerns a many-body deterministic model that displays life-like properties as emergence, complexity, self-organization, spontaneous compartmentalization, and self-regulation. The model portraits the dynamics of an ensemble of…
Autocatalysis underlies the ability of chemical and biochemical systems to replicate. Recently, Blokhuis et al. gave a stoechiometric definition of autocatalysis for reaction networks, stating the existence of a combination of reactions…
Self-replicability is the unique attribute observed in all the living organisms and the question how the life was physically initiated could be equivalent to the question how self-replicating informative polymers were formed in the abiotic…
Evolution produces complex and structured networks of interacting components in chemical, biological, and social systems. We describe a simple mathematical model for the evolution of an idealized chemical system to study how a network of…
The emergence of an autocatalytic network from an available set of elements is a fundamental step in early evolutionary processes, such as the origin of metabolism. Given a set of elements, the reactions between them (chemical or…
Protocells are supposed to have played a key role in the self-organizing processes leading to the emergence of life. Existing models either (i) describe protocell architecture and dynamics, given the existence of sets of collectively…
Local interactions among biomolecules, and the role played by their environment, have gained increasing attention in modelling biochemical reactions. By defining the automaton of molecular perceptions, we explore an agent-based…
In a complex system, the interactions between individual agents often lead to emergent collective behavior like spontaneous synchronization, swarming, and pattern formation. The topology of the network of interactions can have a dramatic…
Living systems contain intricate biochemical networks whose structure is closely related to their function and allows them to exhibit robust behavior in the presence of external stimuli. Such networks typically involve catalytic enzymes,…
Graph Theoretic Process Network Synthesis is described as an introduction to biological networks. Genetic, protein and metabolic systems are considered. The theoretical work of Kauffman is discussed and amplified by critical property…
Complex network dynamics have been analyzed with models of systems of coupled switches or systems of coupled oscillators. However, many complex systems are composed of components with diverse dynamics whose interactions drive the system's…
This chapter is an overview of foundational results in the mathematical theory of replicator systems. Its primary aim is to provide a unified framework for the mathematical formalisation of evolutionary processes in the spirit of…
Biochemical networks are used in computational biology, to model the static and dynamical details of systems involved in cell signaling, metabolism, and regulation of gene expression. Parametric and structural uncertainty, as well as…
We study the dynamics of a system made up of particles of two different species undergoing irreversible quadratic autocatalytic reactions: $A + B \to 2A$. We especially focus on the reaction velocity and on the average time at which the…
This study introduces a novel theoretical framework, the Stacked Autoencoder Evolution Hypothesis, which proposes that biological evolutionary systems operate through multi-layered self-encoding and decoding processes, analogous to stacked…
Motivated by the theory of reaction kinetics based on nonequilibrium thermodynamics and the linear stability of driven reaction-diffusion, we apply the Fokker-Planck equation to describe the population dynamics of an ensemble of reactive…
Large molecules such as proteins and nucleic acids are crucial for life, yet their primordial origin remains a major puzzle. The production of large molecules, as we know it today, requires good catalysts, and the only good catalysts we…
In living cells, chemical reactions form a complex network. Complicated dynamics arising from such networks are the origins of biological functions. We propose a novel mathematical method to analyze bifurcation behaviors of a reaction…
The notion of (auto) catalytic networks has become a cornerstone in understanding the possibility of a sudden dramatic increase of diversity in biological evolution as well as in the evolution of social and economical systems. Here we study…
In this paper, we propose a new method to identify biochemical reaction networks (i.e. both reactions and kinetic parameters) from heterogeneous datasets. Such datasets can contain (a) data from several replicates of an experiment performed…